Another idea is for the two vessels to fly along side the larger ship, with the pointy end wave-guides being outer-most to either side of the main starship...

Would they be attached in some way? Or just flying in formation?

Hmmm... with fancy "tractor beams" and "structural integrity fields" and all that sort of stuff already floating around the world of Star Trek... I don't see any reason why component parts of a spaceship can't be held together by anything more than energy.